What antivirus or popup blocking software are you using? Is this all? Can you give me / PM me the site url so i can have a look?

PM would be better just incase you are infected.

This is a pretty massive subject. Have you had a look at the php documentation for this yet?

How about copy the excel cheets over to anouther server automatically with php so you already have a back up. Then when people upload the excel sheets check weather they are there or not, if they are...